Last updated: 2025-09-23 Version: 0.9.3
Coverage and total number of variants
  • Sample name: HCC1395_60_30
  • Mean tumor coverage (fold): 58.09
  • Estimated tumor mutation burden, TMB
    • WGS by default, or supplied region bed
      • All mutations: 19.775 mut/Mbp
      • Nonsynonymous mutations: 12.382 mut/Mbp
      • Eligible region used for estimation: 2863.232161 Mbp
    • Gencode coding regions
      • All mutations: 16.057 mut/Mbp
      • Nonsynonymous mutations: 11.392 mut/Mbp
      • Eligible region used for estimation: 34.938079 Mbp
  • Total number of small variants: 77505
    • Total number of SNV: 74494
    • Total number of small deletion: 2675
    • Total number of small insertion: 334
  • Total number of structural variants (SV): 1653
BND DEL DUP INS INV
450 546 239 106 2
Tumor purity and ploidy
  • Note that purity and ploidy estimation can be unreliable at low coverage (<30X) and low tumor purity (<50%)
  • Estimated tumor purity and ploidy solutions from Wakhan:
ploidy purity confidence
2.76 1.00 0.72
2.61 0.81 0.69
1.36 0.27 0.36
1.44 0.35 0.36
Micro-satellite instability score (MSI)
  • Micro-satellite instability score (MSI) was estimated using owl.
  • Empirically, >10% unstable sites has been observed in MSI-high samples, but this can differ across cancer types and samples.
Sample Unstable sites Stable sites Percentage unstable Profiled sites Sites passing QC Percentage passing QC
HCC1395_60_30 1054 53413 1.94 47228 29355 62.16 pass
CNV Table — Haplotype 1 (cnv1)
CNV Table — Haplotype 2 (cnv2)
Small variants (SNV/INDEL) coverage and variant allele frequency (VAF) distribution
Mutational signatures
  • Mutational signature is estimated using R package MutationalPattern based on SNVs only (INDELs are ignored).
Notes on small variants (SNV/INDEL) filtering
  • Variants are filtered with any of the following criteria:
    • IMPACT is HIGH or MODERATE
    • CLIN_SIG contains pathogenic (Pathogenic intron variants will be retained)
    • CANCER_TYPE is not NA (variants that are in IntOGen Cancer Gene Census)
    • MAX_AF (maximum population allele frequency) is less than 3%
  • CANCER_TYPE_ROLE and CANCER_TYPE_CGC_GENE are merged columns from CANCER_TYPE, ROLE and CGC_CANCER_GENE. These columns are collapsed into single entries separated by semicolon. E.g. CANCER_TYPE = “Breast;Prostate” and ROLE - “LoF;Act” means that the gene is a LoF in breast cancer and an Act in prostate cancer. This is done so that the table is more readable.
Small variants (SNV/INDEL) table
Notes on structural variants (SVs)
  • SVs are filtered to only those that are part of the IntOGen Cancer Gene Census (CGC)
  • Annotation based on AnnotSV. However to make the output readable some columns with very long information (e.g. “_coord” and “_source”) are removed. Please refer to original AnnotSV output for more information.
    • AnnotSV converts square bracketed notation using the harmonization rule from variant-extractor, which may result in wrong conversion, especially in BND to DEL conversion.
  • Capital letter columns are from IntOGen CGC. Please see README from the IntOGen release for more information.
    • CANCER_TYPE_ROLE and CANCER_TYPE_CGC_GENE are merged columns from CANCER_TYPE, ROLE and CGC_CANCER_GENE. These columns are collapsed into single entries separated by semicolon. E.g. CANCER_TYPE = “Breast;Prostate” and ROLE - “LoF;Act” means that the gene is a LoF in breast cancer and an Act in prostate cancer. This is done so that the table is more readable.
  • Each SV can affect multiple genes. AnnotSV “splits” the different genes into different entries. This is why there are multiple rows with the same AnnotSV_ID.
  • ALT allele for insertion is hidden as “Too long” in the table. Please refer to the original AnnotSV output for more information.
  • Note that Severus can call duplication as BND event, and AnnotSV has a tendency to annotate these as DEL event since it doesn’t make use of the “STRAND” information. Therefore, the “SV_type” column is not very accurate for BND events (You will recognize these with SEVERUS_BND in the ID column)
  • The “SAMPLE” column represents the FORMAT column in the VCF. For Severus this is “GT:GQ:VAF:hVAF:DR:DV”
  • Translocations are defined as all BND pairs that are at least 100kbp apart:
    • Limitation: It is possible for large duplication or deletion events to be called as BND events.
  • BND pairs are connected by a line:
    • Red line: BND pairs that are in the Mitelman fusion database (>= 3 samples).
    • Black line: BND pairs involving known genes supplied to svpack GFF.
    • Grey line: All other BND pairs.
  • Note that genes that are within 8 Mbp of each other are merged into a single group with a “/” separator.
circos plot
  • This table contains all genes pairs with one gene documented in the Mitelman fusion database (>= 3 samples).